Lecithin cholesteryl acyltransferase (LCAT) is a 63 Kd enzyme that is responsible for the esterification of virtually all free cholesterol in plasma. Patients with functional defects in LCAT present with profound hypoalphalipoproteinemia establishing an important role for LCAT in HDL metabolism. We have identified a novel mutation in the LCAT gene of a French patient presenting with corneal opacities and HDL-C levels of less than 10 mg/dl. DNA sequencing and RFLP analysis revealed that the patient is a compound heterozygote for a C to T and C to A mutation resulting in the substitution of Arg 99 to Cys and Tyr 83 to stop, respectively. In vitro expression of the two mutant LCAT established the functional significance of both gene defects. Cholesteryl ester transfer protein (CETP) is responsible for the transfer of neutral lipids between the B-containing lipoproteins and HDL. Although CETP deficiency is a common cause of high HDL in Japan, the genetic basis of this disorder has not been fully characterized. We have studied a patient presenting with TC, HDL-C and apoA-I levels of 300, 236 and 233 mg/dl, respectively and total absence of CETP activity and mass in plasma. Sequence analysis of the patients's gene revealed that the splice donor consensus GT was substituted by GG in intron 10 and by AT in intron 14. Restriction digestion using NdeI and MaeIII established that the pt was a compound heterozygote for both gene defects. Sequencing of RT-PCR amplified DNA from macrophage RNA demonstrated abnormal splicing with deletion of exon 10 as well as alternative splicing at a native AG site located 31 nucleotides 5' of the normal splice acceptor in intron 13. This defect results in the insertion of a 31 bp fragment between exon 13 and exon 14 as well as the introduction of an in frame stop codon. The presence of abnormally spliced mRNA was further confirmed by amplification of patient RT-PCR DNA using CETP specific primers thus establishing the functional significance of these defects.